› 6yjr

X-ray diffraction
2.2Å resolution

Crystal structure of unliganded MGAT5 (alpha-1,6-mannosylglycoprotein 6-beta-N-acetylglucosaminyltransferase V) luminal domain.

Released:
DOI: 10.2210/pdb6yjr/pdb
PDB entry 6yjr coloured by chain, front view.
PDB entry 6yjr coloured by chain, side view.
PDB entry 6yjr coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
Substrate Engagement and Catalytic Mechanisms of N-Acetylglucosaminyltransferase V
Darby JF, Gilio AK, Piniello B, Roth C, Blagova E, Rovira C, Hubbard RE, Davies GJ, Wu L
ACS Catalysis (2020)

Function and Biology Details

Reaction catalysed: 
UDP-N-acetyl-alpha-D-glucosamine + beta-D-GlcNAc-(1->2)-(beta-D-GlcNAc-(1->4))-alpha-D-Man-(1->3)-(beta-D-GlcNAc-(1->2)-alpha-D-Man-(1->6))-beta-D-Man-(1->4)-beta-D-GlcNAc-(1->4)-beta-D-GlcNAc-N-Asn-[protein] = UDP + beta-D-GlcNAc-(1->2)-(beta-D-GlcNAc-(1->4))-alpha-D-Man-(1->3)-[beta-D-GlcNAc-(1->2)-(beta-D-GlcNAc-(1->6))-alpha-D-Man-(1->6)]-beta-D-Man-(1->4)-beta-D-GlcNAc-(1->4)-beta-D-GlcNAc-N-Asn-[protein]
Biochemical function:
Biological process:
Cellular component:
  • not assigned
Sequence domain:

Structure analysis Details

Assembly composition:
monomeric (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-170784 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecules (2 distinct):
Secreted alpha-1,6-mannosylglycoprotein 6-beta-N-acetylglucosaminyltransferase A Chains: AAA, BBB
Molecule details ›
Chains: AAA, BBB
Length: 528 amino acids
Theoretical weight: 60.54 KDa
Source organism: Homo sapiens
Expression system: Trichoplusia ni
UniProt:
  • Canonical: Q09328 (Residues: 214-741; Coverage: 71%)
Gene names: GGNT5, MGAT5
Sequence domains: Glycosyltransferase family 18

Ligands and Environments

Carbohydrate polymer : NEW Components: NAG, FUC
Carbohydrate polymer
2 bound ligands:
Ligand NAG 1 x NAG
Ligand EDO 4 x EDO
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: DIAMOND BEAMLINE I03
Spacegroup: P212121
Unit cell:
a: 59.809Å b: 100.415Å c: 207.981Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.211 0.208 0.262
Expression system: Trichoplusia ni

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